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Updated: May 28, 2025

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
Published on: December 16, 2013
1H isotropic chemical shift metrics for NMR crystallography of powdered molecular organics
Fatemeh Zakeri1, Cory M Widdifield1
1Department of Chemistry & Biochemistry, University of Regina, 3737 Wascana Pkwy, Regina, SK S4S 0A2, Canada. cory.widdifield@uregina.ca.
Abstract:
Hydrogen magnetic shielding values from gauge including projector augmented wave (GIPAW) density functional theory (DFT) calculations, when combined with experimental solid-state 1H nuclear magnetic resonance (NMR) chemical shift data collected on powdered microcrystalline organics, have been used to perform various crystal structure characterization tasks (e.g., refinements, verifications, determinations). These tasks fall under the umbrella of 'NMR crystallography'. In several instances, an isotropic 1H chemical shift (δiso) root-mean-squared deviation (RMSD) metric has been applied during these studies (including the first de novo crystal structure determination: M. Baias, J.-N. Dumez, P. H. Svensson, S. Schantz, G. M. Day and L. Emsley, De Novo Determination of the Crystal Structure of a Large Drug Molecule by Crystal Structure Prediction-Based Powder NMR Crystallography, J. Am. Chem. Soc., 2013, 135, 17501-17507). While it is assumed that the 1H δiso RMSD metrics are converged, our study probes the robustness of these metrics. Specifically, we consider how the structure of the δiso(1H) RMSD metric varies depending on: (i) selected GIPAW DFT input parameters; (ii) the number of fitting parameters used during linear mapping; and (iii) the GIPAW DFT computational software. These δiso(1H) RMSD metrics were produced from a set of 24 benchmark crystal structures (428 crystallographically unique hydrogen atom environments). Interestingly, we find that the δiso(1H) RMSD metric structures are very robust to substantial degradation in the quality of the GIPAW DFT computations, which is unexplored in the NMR crystallography literature as prior studies focus on convergence rather than divergence. We then briefly consider the impact of our findings using the structure determination of thymol as an illustrative example and our results strongly suggest that if δiso(1H) RMSD metrics are being used, then the GIPAW DFT computations can be performed much more efficiently than at present. Overall, this should allow for more efficient NMR crystallography characterization tasks of important materials that contain 1H nuclei, such as organic pharmaceuticals.
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